File size: 7,622 Bytes
2c3c408 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 | #include <tiledb/tiledb.h> // for enums
#include <tiledb/tiledb> // C++
#include "common.h"
#include <pybind11/numpy.h>
#include <pybind11/pybind11.h>
#include <pybind11/pytypes.h>
#include <pybind11/stl.h>
namespace libtiledbcpp {
using namespace tiledb;
namespace py = pybind11;
void init_array(py::module &m) {
py::class_<tiledb::Array>(m, "Array")
//.def(py::init<py::object, py::object, py::iterable, py::object,
// py::object, py::object>())
.def(
py::init<const Context &, const std::string &, tiledb_query_type_t>(),
py::keep_alive<1, 2>() /* Array keeps Context alive */)
// Temporary initializer while Array is converted from Cython to PyBind.
.def(py::init([](const Context &ctx, py::object array) {
tiledb_array_t *c_array = (py::capsule)array.attr("__capsule__")();
return std::make_unique<Array>(ctx, c_array, false);
}),
py::keep_alive<1, 2>(), py::keep_alive<1, 3>())
// TODO capsule Array(const Context& ctx, tiledb_array_t* carray,
// tiledb_config_t* config)
.def("is_open", &Array::is_open)
.def("uri", &Array::uri)
.def("schema", &Array::schema)
//.def("ptr", [](Array& arr){ return py::capsule(arr.ptr()); } )
.def("open", (void(Array::*)(tiledb_query_type_t)) & Array::open)
.def("reopen", &Array::reopen)
.def("set_open_timestamp_start", &Array::set_open_timestamp_start)
.def("set_open_timestamp_end", &Array::set_open_timestamp_end)
.def_property_readonly("open_timestamp_start",
&Array::open_timestamp_start)
.def_property_readonly("open_timestamp_end", &Array::open_timestamp_end)
.def("set_config", &Array::set_config)
.def("config", &Array::config)
.def("close", &Array::close)
.def("consolidate",
[](Array &self, const Context &ctx, Config *config) {
if (self.query_type() == TILEDB_READ) {
throw TileDBError("cannot consolidate array opened in readonly "
"mode (mode='r')");
}
Array::consolidate(ctx, self.uri(), config);
})
.def("consolidate",
[](Array &self, const Context &ctx,
const std::vector<std::string> &fragment_uris, Config *config) {
if (self.query_type() == TILEDB_READ) {
throw TileDBError("cannot consolidate array opened in readonly "
"mode (mode='r')");
}
std::vector<const char *> c_strings;
c_strings.reserve(fragment_uris.size());
for (const auto &str : fragment_uris) {
c_strings.push_back(str.c_str());
}
Array::consolidate(ctx, self.uri(), c_strings.data(),
fragment_uris.size(), config);
})
.def("consolidate",
[](Array &self, const Context &ctx,
const std::tuple<int, int> ×tamp, Config *config) {
if (self.query_type() == TILEDB_READ) {
throw TileDBError("cannot consolidate array opened in readonly "
"mode (mode='r')");
}
int start, end;
std::tie(start, end) = timestamp;
config->set("sm.consolidation.timestamp_start",
std::to_string(start));
config->set("sm.consolidation.timestamp_end", std::to_string(end));
Array::consolidate(ctx, self.uri(), config);
})
.def("vacuum", &Array::vacuum)
.def("create",
py::overload_cast<const std::string &, const ArraySchema &>(
&Array::create))
.def("load_schema",
py::overload_cast<const Context &, const std::string &>(
&Array::load_schema))
.def("encryption_type", &Array::encryption_type)
// TODO non_empty_domain
// TODO non_empty_domain_var
.def("query_type", &Array::query_type)
.def("consolidate_fragments",
[](Array &self, const Context &ctx,
const std::vector<std::string> &fragment_uris, Config *config) {
std::vector<const char *> c_strings;
c_strings.reserve(fragment_uris.size());
for (const auto &str : fragment_uris) {
c_strings.push_back(str.c_str());
}
ctx.handle_error(tiledb_array_consolidate_fragments(
ctx.ptr().get(), self.uri().c_str(), c_strings.data(),
fragment_uris.size(), config->ptr().get()));
})
.def("consolidate_metadata",
py::overload_cast<const Context &, const std::string &,
Config *const>(&Array::consolidate_metadata))
.def("put_metadata",
[](Array &self, std::string &key, tiledb_datatype_t tdb_type,
const py::buffer &b) {
py::buffer_info info = b.request();
// size_t size = std::reduce(info.shape.begin(),
// info.shape.end());
size_t size = 1;
for (auto s : info.shape) {
size *= s;
}
// size_t nbytes = size * info.itemsize;
self.put_metadata(key, tdb_type, size, info.ptr);
/*
std::cout << "ndim: " << info.ndim << std::endl;
std::cout << "sz: " << size << std::endl;
std::cout << "imsz: " << info.itemsize << std::endl;
std::cout << "--|" << std::endl;
for (auto& s : info.shape) {
std::cout << s << std::endl;
}
*/
})
.def("get_metadata",
[](Array &self, std::string &key) -> py::buffer {
tiledb_datatype_t tdb_type;
uint32_t value_num = 0;
const void *data_ptr = nullptr;
self.get_metadata(key, &tdb_type, &value_num, &data_ptr);
if (data_ptr == nullptr && value_num != 1) {
throw py::key_error();
}
assert(data_ptr != nullptr);
return py::memoryview::from_memory(
data_ptr, value_num * tiledb_datatype_size(tdb_type));
})
.def("get_metadata_from_index",
[](Array &self, uint64_t index) -> py::tuple {
tiledb_datatype_t tdb_type;
uint32_t value_num = 0;
const void *data_ptr = nullptr;
std::string key;
self.get_metadata_from_index(index, &key, &tdb_type, &value_num,
&data_ptr);
if (data_ptr == nullptr && value_num != 1) {
throw py::key_error();
}
// TODO handle empty value case
assert(data_ptr != nullptr);
auto buf = py::memoryview::from_memory(
data_ptr, value_num * tiledb_datatype_size(tdb_type));
return py::make_tuple(tdb_type, buf);
})
.def("delete_metadata", &Array::delete_metadata)
.def("has_metadata",
[](Array &self, std::string &key) -> py::tuple {
tiledb_datatype_t has_type;
bool has_it = self.has_metadata(key, &has_type);
return py::make_tuple(has_it, has_type);
})
.def("metadata_num", &Array::metadata_num)
.def("delete_array",
py::overload_cast<const Context &, const std::string &>(
&Array::delete_array));
}
} // namespace libtiledbcpp
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